I've Neural Prod and Elemental Burst both as Mage Legendaries and can't get either to show as available abilities or they show as always available even when on CD. I know this started as a problem during PTS, but I heard somewhere that the developer was in the process of fixing it.

Try making the alerts again; there was a bug with the Cooldown events firing (which is what caused problems for kalert) that was fixed in Thursday's patch.